Background: The eMERGE III Network was tasked with harmonizing genetic testing protocols linking multiple sites and investigators. Methods: DNA capture panels targeting 109 genes and 1551 variants were constructed by two clinical sequencing centers for analysis of 25,000 participant DNA samples collected at 11 sites where samples were linked to patients with electronic health records. Each step from sample collection, data generation, interpretation, reporting, delivery and storage, were developed and validated in CAP/CLIA settings and harmonized across sequencing centers. Results: A compliant and secure network was built and enabled ongoing review and reconciliation of clinical interpretations while maintaining communication and data sharing between investigators. Mechanisms for sustained propagation and growth of the network were established. An interim data freeze representing 15,574 sequenced subjects, informed the assay performance for a range of variant types, the rate of return of results for different phenotypes and the frequency of secondary findings. Practical obstacles for implementation and scaling of clinical and research findings were identified and addressed. The eMERGE protocols and tools established are now available for widespread dissemination. Conclusions: This study established processes for different sequencing sites to harmonize the technical and interpretive aspects of sequencing tests, a critical achievement towards global standardization of genomic testing. The network established experience in the return of results and the rate of secondary findings across diverse biobank populations. Furthermore, the eMERGE network has accomplished integration of structured genomic results into multiple electronic health record systems, setting the stage for clinical decision support to enable genomic medicine.
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